TobaccoSeeds
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB31125 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3224030.fastq.gz | Fastqsanger.gz | |||
| ERR3224040.fastq.gz | Fastqsanger.gz | |||
| ERR3224031.fastq.gz | Fastqsanger.gz | |||
| ERR3224041.fastq.gz | Fastqsanger.gz | |||
| ERR3224032.fastq.gz | Fastqsanger.gz |
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Project description:2 MudPIT analysis of tobacco seeds. MGF files made with Bioworks 3.3.1. Not published.
2019-05-20 | MSV000083831 | MassIVE
Project description:MicroRNAs and siRNAs are important regulators of plant development and seed formation, yet their population and abundance in the oil crop Brassica napus are still less understood, especially at different developmental stages and among cultivars with varied seed oil contents. Here, we systematically analyzed the small RNA expression profiles of Brassica napus seeds at early embryonic developmental stages in a high oil content and a low oil content Brassica napus cultivars, both cultured in two environments. A total of 50 conserved miRNAs and 11 new miRNAs were identified, together with some new miRNA targets. Expression analysis revealed some miRNAs with varied expression levels in different seed oil content cultivars or at different embryonic developmental stages. A large amount of 23-nt small RNAs with specific nucleotide composition preference were also identified, which may present new classes of functional small RNAs.
2011-12-28 | GSE34727 | GEO
Project description:Rice is a major component of the human diet and feeds more than 50 million people across the globe. Therefore, efforts are being made to improve the nutritional quality of rice seeds in order to make a super-rice cultivar rich in antioxidants and vitamins. We previously developed two rice cultivars, Super-hongmi (red seeds) and Super-jami (black seeds), that were highly rich in antioxidants and exhibited high levels of radical scavenging activities. However, the molecular mechanism underlying the color development and accumulation of different antioxidants in these rice cultivars remains largely elusive. Here, we report the proteome profiles of mature Super-hongmi, and Super-jami seeds and compared with the Hopum (white seeds) using a label-free quantitative proteomics approach. This approach led to the identification of 5127 rice seed proteins of which 1628 showed significant changes (ANOVA, Benjamini-Hochberg FDR ≤ 0.01, fold change ≥ 1.5). Functional annotation of the differentially modulated proteins led to the identification of a phytoene desaturase (PDS3) that was highly enriched in the red seeds and was decreased in the black seeds as compared to the control white seeds. PDS3 is involved in the conversion of phytoene to ζ-carotene which may be responsible for the accumulation of red color in red seeds. Moreover, black seeds seem to accumulate higher levels of anthocyanins because of the higher abundance of dihydroflavonol 4-reductase. In addition, proteins associated with lignin and tocopherol biosynthesis were found to be highly increased in both red and black cultivars. Taken together, these data report the seed proteome of three different colored rice seeds and identify novel components associated with pigment accumulation.
2023-09-21 | PXD039588 | Pride
Project description:RNA sequencing in sunflower for detect mRNA expression of developmental seeds. The two cultivars (86-1, L-1-OL-1) with significant difference in oleic acid content in two different seed developmental stages (oleic acid accumulated rapidly at 17 DAF, and kept relatively stable at 27 DAF) for transcriptome sequencing
2021-01-01 | GSE164103 | GEO
Project description:Purpose: we conducted a six time-point transcriptomic analysis using two tobacco cultivars with contrasting cold responses, Taiyan8 tobacco (TT, cold susceptibility) and Yanyan97 tobacco (YT, cold resistance). Methods: mRNA profiles of Tobacco seedlings from CK and cold-treated plants were generated by deep sequencing, in triplicate, usingIllumina Hiseq4500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with methods: hisat2 (v2.0.5), SAMtools (v1.9). StringTie (v1.3.4d) and FeatureCounts (v1.6.4) Results: We found that both cultivars had common mechanisms to cope with cold stress, including common differentially expressed genes (DEGs), similar time-point-related differential expression profile of genes, and similar NtCBF gene co-expression modules, suggesting conservation of adaptation strategies for cold responses. Importantly, we found that YT experienced DEGs even under normal growth condition and had less DEGs in early stage of cold stress (0.5-2 h) when compared to TT, reflecting occurrence of genotype-dependent gene transcription. Moreover, a gene co-expression module (brown) with stress-related genes up-regulated in YT instead of TT at late stage (4-8 h), which might contribute to contrasting phenotypic changes during cold stress between TT and YT. Conclusions: our study provides valuable resources for transcriptomic studies of cold responses in plants. It also helps to identify key cold responsive genes for genetic manipulation for breeding of tobacco cultivars in the future.
2022-08-03 | GSE173352 | GEO
Project description:Transcriptome analyses on seeds developed in different parental conditions investigating the effect of the parental environment on the transcriptome of dry seeds of three different genotypes
2016-01-01 | GSE75837 | GEO
Project description:For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficient coverage of genomic sequences, however, none of the expressed sequence tag (EST)-based chips developed to date cover gene expression from the whole genome. The availability of Tobacco Genome Initiative (TGI) sequences provides a useful resource to build a whole genome exon array, even if the assembled sequences are highly fragmented. Here, the design of a Tobacco Exon Array is reported and an application to improve the understanding of genes regulated by cadmium (Cd) in tobacco is described. From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon) and tested on two selected tobacco varieties. Two tobacco varieties out of 45 accumulating low and high cadmium in leaf were identified based on the GGE biplot analysis, which is analysis of the genotype main effect (G) plus analysis of the genotype by environment interaction (GE) of eight field trials (four fields over two years) showing reproducibility across the trials. The selected varieties were grown under greenhouse conditions in two different soils and subjected to exon array analyses using root and leaf tissue to understand the genetic make-up of the Cd accumulation. An Affymetrix Exon Array was developed to cover a large (~90%) proportion of the tobacco gene space. The Tobacco Exon Array will be available for research use through the Affymetrix array catalogue. As a proof of the exon array usability, we have demonstrated that the Tobacco Exon Array is a valuable tool for studying Cd accumulation in tobacco leaves. Data from field and greenhouse experiments supported by gene expression studies strongly suggested that the difference in leaf Cd accumulation between the two specific tobacco cultivars is dependent solely on genetic factors and genetic variability rather than on the environment. 22 samples were used with 3 different experimental factors: [1] 2 different tissues (leaves and roots/lateral), [2] 2 different mutations (V5 and V21), and [3] 2 different stimuli (Soil 1 and Soil 2). 2-3 biological replicates were used. One sample did not pass QC and is not included in this submission.
2012-11-16 | E-GEOD-42319 | biostudies-arrayexpress